I have not watched the Pokémon anime since Battle Frontier, but I saw a snippet of a much newer episode in a region that is most definitely not Johto, that featured Claire, the Dragon gym leader from the Johto region.

This led me to realize that it's not impossible that the anime producers would bring back characters from the very distant past.

So I was thinking, does Ash ever re-encounter his Butterfree in an episode after Butterfree's Goodbye?

Ash has never met his Butterfree again yet (at the time I'm posting). We can only see him in some flashbacks and in the tenth opening of the anime.
– IsukaJan 25 '16 at 11:37

One episode was conjectured by fans to take this form, but in the end it didn't. Instead it had Ash befriend a Metapod that, in that same episode, evolved into a Butterfree that didn't ultimately stay with him.
– J.G.Jan 25 '16 at 16:26

With butterfree I'm assuming it died. If it's anything like a real life butterfly or insects in general they have short life spans, real butterflies depending on the type live from a few weeks to a year at most. Considering how in pokemon insect types evolve the fastest and are found in bulk it should correlate they die the youngest and lay many eggs to compensate like real life insects as well.